Local analysis
==============

If you are interested in running your analysis locally and storing the
results to the server, then your first step is to become familiar with
the developer documentation.

-  The :doc:`/developers/GettingStarted` guide provides numerous examples in 
   each 
   language with explanations and tries to be a starting point for anyone who 
   wants to write code which talks to the OMERO server.
-  Most of the :doc:`/developers/Modules/Api` is covered by the 
   :javadoc:`Javadocs <>`.
-  Each of the languages has extra information on its own page:

   -  |OmeroCpp|
   -  |OmeroJava|
   -  |OmeroMatlab|
   -  |OmeroPy|


Once you have your local analysis working, you can push it onto the server for 
background processing using the 
:doc:`OMERO scripting service <scripts/index>`.


.. _omerotables:

Storing external data in OMERO
==============================

There are several options for storing external or schema-less data in OMERO,
including
:doc:`StructuredAnnotations </developers/Model/StructuredAnnotations>`
for small quantities of data, or extending the OME model, but this risks
interoperability issues. (See
:doc:`ExtendingOmero </developers/Server/ExtendingOmero>`).

For larger volumes of data, or data which needs to be queried,
:doc:`/developers/Tables` provides a unified and effective solution for the storage of
tabular data from various sources, such as automated analysis results or
script-based processing, and makes them available within OMERO.


Third-party analysis and OMERO.tables
-------------------------------------

Support has been added for some third-party analysis data, which gets 
converted in OMERO into a common format. These formats include:

-  MIAS data, measurements, and overlays
-  InCell data and measurements
-  Flex data with Acapella results
   (:snapshot:`screencast <movies/omero-4-1/mov/FlexPreview4.1-import.mov>`).
   In the Flex case, additional configuration may be necessary for
   accessing both the raw data and the analysis results. Watch :snapshot:`the 
   configuration screencast 
   <movies/omero-4-1/mov/FlexPreview4.1-configuration.mov>` for more 
   information.

The analysis results which are parsed out of the formats listed above are 
converted to HDF by the OMERO.tables API. This
facility can then be used by clients to visualize the parsed measurements, and 
in the case of regions of interest, see their location overlayed on the 
associated image:

.. figure:: /images/MeasurementToolSep09.png
  :align: center
  :alt: Measurement Tool


Other high-content screening (HCS) data
---------------------------------------

In addition to the Flex, Mias, and InCell 100 file formats, BD Pathway, 
Olympus ScanR, and native OME-XML/TIFF files can all be imported as HCS 
data, though without support for any external analysis data which may be 
attached. If you are interested in having other analysis formats supported, 
contact either the :doc:`open source community </users/community-resources>` 
or |Glencoe| depending on your needs.
